--- a/pathway_image.xml	Tue Oct 23 14:38:04 2012 -0400
+++ b/pathway_image.xml	Mon Nov 05 12:44:17 2012 -0500
@@ -6,15 +6,15 @@
       "--input=${input}"
       "--output=${output}"
       "--KEGGpath=${pathway}"
-      "--posKEGGclmn=${input.metadata.kegg_path}"
-      "--KEGGgeneposcolmn=${input.metadata.kegg_gene}"
+      "--posKEGGclmn=${kpath}"
+      "--KEGGgeneposcolmn=${kgene}"
   </command>
 
   <inputs>
-    <param name="input" type="data" format="gd_sap" label="Table">
-      <validator type="metadata" check="kegg_gene,kegg_path" message="Missing KEGG gene code column and/or KEGG pathway code/name column metadata.  Click the pencil icon in the history item to edit/save the metadata attributes" />
-    </param>
-    <param name="pathway" type="select">
+    <param name="input" type="data" format="tabular" label="Dataset" />
+    <param name="kgene" type="data_column" data_ref="input" label="Column with KEGG gene ID"  />
+    <param name="kpath" type="data_column" data_ref="input" numerical="false" label="Column with KEGG pathways" />
+    <param name="pathway" label="Pathway" type="select">
       <options from_file="gd.pathways.txt">
         <column name="value" index="1"/>
         <column name="name" index="2"/>
@@ -30,6 +30,8 @@
   <tests>
     <test>
       <param name="input" value="test_in/sample.gd_sap" ftype="gd_sap" />
+      <param name="kpath" value="10" />
+      <param name="kgene" value="12" />
       <param name="pathway" value="cfa05214" />
       <output name="output" file="test_out/pathway_image/pathway_image.png" compare="sim_size" delta = "10000" />
     </test>
@@ -37,12 +39,45 @@
 
   <help>
 
+**Dataset formats**
+
+The input and output datasets are in tabular_ format.
+The input dataset must have columns with KEGG gene ID and pathways.
+The output dataset is described below.
+(`Dataset missing?`_)
+
+.. _tabular: ./static/formatHelp.html#tab
+.. _Dataset missing?: ./static/formatHelp.html
+
+-----
+
 **What it does**
 
-This tool produces an image of an input KEGG pathway, highlighting the
-modules representing genes in an input list.  NOTE:  a given gene can
+This tool produces an image of a KEGG pathway, highlighting (in red) the
+modules representing genes in the input dataset.  Click here_ for help
+with reading the pathway map.
+
+NOTE:  a given gene can
 be assigned to multiple modules, and different genes can be assigned to
 the same module.
 
+.. _here: http://www.genome.jp/kegg/document/help_pathway.html
+
+-----
+
+**Example**
+
+- input::
+
+   476153  probably damaging       cfa00230=Purine metabolism.cfa00500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways
+   483960  probably damaging       N
+   610160  possibly damaging       N
+   403657  benign  cfa04010=MAPK signaling pathway.cfa04012=ErbB signaling pathway.cfa04060=Cytokine-cytokine receptor interaction.cfa04144=Endocytosis.cfa04510=Focal adhesion.cfa04540=Gap junction.cfa04810=Regulation of actin cytoskeleton.cfa05160=Hepatitis C.cfa05200=Pathways in cancer.cfa05212=Pancreatic cancer.cfa05213=Endometrial cancer.cfa05214=Glioma.cfa05215=Prostate cancer.cfa05218=Melanoma.cfa05219=Bladder cancer.cfa05223=Non-small cell lung cancer
+   etc.
+
+output showing pathway cfa05214:
+
+.. image:: ${static_path}/images/gd_pathway_image.png
+
   </help>
 </tool>